Package org.biojava.bio.alignment

Class FlexibleAlignment

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbolList

org.biojava.bio.alignment.AbstractULAlignment

org.biojava.bio.alignment.FlexibleAlignment

All Implemented Interfaces:

Alignment, ARAlignment, EditableAlignment, UnequalLengthAlignment, SymbolList, Changeable

public class FlexibleAlignment
extends AbstractULAlignment
implements ARAlignment, EditableAlignment

FlexibleAlignment is a class which implements UnequalLengthAlignment, ARAlignment and EditableAlignment It places no restriction on where any sequence can be in the alignment so there could be gaps in the alignment. You tell it where to put the sequence, it will do it. I think I will be adding an Exception NonContinuousAlignmentException. STILL UNDER CONSTRUCTION. seqString does not work because there it does not seem to support tokenization 'token' this is true for SimpleAlignment too.

Author:

David Waring, Matthew Pocock

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.bio.alignment.AbstractULAlignment

AbstractULAlignment.LeftRightLocationComparator<T>, AbstractULAlignment.SubULAlignment

Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList

AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater

Nested classes/interfaces inherited from interface org.biojava.bio.alignment.Alignment

Alignment.SymbolListIterator

Field Summary

Fields

Modifier and Type	Field	Description
protected Location	alignmentRange
protected Map<Object,AlignmentElement>	data
protected List<String>	labelOrder

Fields inherited from class org.biojava.bio.alignment.AbstractULAlignment

alphabet

Fields inherited from interface org.biojava.bio.alignment.Alignment

CONTENT

Fields inherited from interface org.biojava.bio.alignment.ARAlignment

ADD_LABEL, REMOVE_LABEL

Fields inherited from interface org.biojava.bio.alignment.EditableAlignment

GAPS, LOCATION

Fields inherited from interface org.biojava.bio.symbol.SymbolList

EDIT, EMPTY_LIST

Constructor Summary

Constructors

Constructor	Description
FlexibleAlignment(List<AlignmentElement> seqList)	construct this object with the reference sequence which can either be a gappedSymbolList or not label in all cases refers to an object that holds the display name (generally just a String). since more than one sequence in an alignment could have the same name this works as long as the labels are different objects even though they may hold the same name.

Method Summary

Modifier and Type	Method	Description
void	addSequence(AlignmentElement ae)	add a new a alignment usings a location to the reference sequence.
protected boolean	allGaps(SymbolList seq, int start, int end)	make sure that all Symbols in this range are gaps
void	edit(Object label, Edit edit)	edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.
protected AlignmentElement	getAE(Object label)
Alphabet	getAlphabet()	The alphabet that this SymbolList is over.
List<String>	getLabels()	getLabels will return a list of labels in left to right order
List<Object>	getLabelsAt(int column)
protected int	greater(int x, int y)
int	length()	The number of symbols in this SymbolList.
protected int	lesser(int x, int y)
Location	locInAlignment(Object label)	The location of an individual SymbolList relative to overall Alignment
protected Location	locInSeq(Object label, Location viewLoc)
protected int	posInSeq(Object label, int column)	get the position in the sequence corresponding to the postion within the alignment
void	removeGaps(GappedSymbolList seq, int start, int length)	because there is a bug in GappedSymbolList
void	removeSequence(Object label)
protected void	resetRange()	check that begining is at 1 otherwise shift everything over
protected void	shift(Object label, int offset)	moves the whole sequence
protected void	shiftAll(int offset)
void	shiftAtAlignmentLoc(Object label, Location loc, int offset)	loc in this case is the Alignment Location
void	shiftAtSequenceLoc(Object label, Location loc, int offset)	loc in this case is the SymbolList Location
Symbol	symbolAt(String label, int column)	This gets the symbol for an individual sequence at position in the overall alignment If the sequence is not aligned at that location it returns null
SymbolList	symbolListForLabel(String label)	Retrieve a single row of the alignment by label.

Methods inherited from class org.biojava.bio.alignment.AbstractULAlignment

debug, labelsAt, labelsInRange, leftMost, orderedLables, rightMost, subAlignment, subAlignment, symbolAt, symbolListIterator

Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList

edit, equals, hashCode, iterator, seqString, subList, subStr, toList, toString

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.bio.alignment.Alignment

subAlignment, symbolListIterator

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.symbol.SymbolList

edit, iterator, seqString, subList, subStr, symbolAt, toList

Field Detail

data

protected Map<Object,AlignmentElement> data

labelOrder

protected List<String> labelOrder

alignmentRange

protected Location alignmentRange

Constructor Detail

FlexibleAlignment

public FlexibleAlignment(List<AlignmentElement> seqList)
                  throws BioException

construct this object with the reference sequence which can either be a gappedSymbolList or not label in all cases refers to an object that holds the display name (generally just a String). since more than one sequence in an alignment could have the same name this works as long as the labels are different objects even though they may hold the same name.

Throws:

BioException

Method Detail

addSequence

public void addSequence(AlignmentElement ae)
                 throws ChangeVetoException,
                        BioException

add a new a alignment usings a location to the reference sequence. This should either contain no gaps or it should be relative to a reference sequence that already has the gaps added

Specified by:

addSequence in interface ARAlignment

Throws:

ChangeVetoException

BioException

removeSequence

public void removeSequence(Object label)
                    throws ChangeVetoException

Specified by:

removeSequence in interface ARAlignment

Throws:

ChangeVetoException

locInAlignment

public Location locInAlignment(Object label)
                        throws NoSuchElementException

The location of an individual SymbolList relative to overall Alignment

Specified by:

locInAlignment in interface UnequalLengthAlignment

Throws:

NoSuchElementException

getLabelsAt

public List<Object> getLabelsAt(int column)
                         throws IndexOutOfBoundsException

Throws:

IndexOutOfBoundsException

length

public int length()

Description copied from interface: SymbolList

The number of symbols in this SymbolList.

Specified by:

length in interface SymbolList

Returns:

the length

getAlphabet

public Alphabet getAlphabet()

Description copied from interface: SymbolList

The alphabet that this SymbolList is over.

Every symbol within this SymbolList is a member of this alphabet. alphabet.contains(symbol) == true for each symbol that is within this sequence.

Specified by:

getAlphabet in interface SymbolList

Returns:

the alphabet

getLabels

public List<String> getLabels()

getLabels will return a list of labels in left to right order

Specified by:

getLabels in interface Alignment

Returns:

the List of all SymbolLists in the alignment

symbolAt

public Symbol symbolAt(String label,
                       int column)
                throws NoSuchElementException,
                       IndexOutOfBoundsException

This gets the symbol for an individual sequence at position in the overall alignment If the sequence is not aligned at that location it returns null

Specified by:

symbolAt in interface Alignment

Parameters:

label - the SymbolList to retrieve from

column - the index of the column to retrieve

Returns:

the symbol in the symbol list associated with the label at the given column

Throws:

NoSuchElementException - if there is no row for 'label'

IndexOutOfBoundsException

symbolListForLabel

public SymbolList symbolListForLabel(String label)
                              throws NoSuchElementException

Description copied from interface: Alignment

Retrieve a single row of the alignment by label.

Specified by:

symbolListForLabel in interface Alignment

Parameters:

label -

Returns:

Throws:

NoSuchElementException

edit

public void edit(Object label,
                 Edit edit)
          throws ChangeVetoException

Description copied from interface: EditableAlignment

edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.

Specified by:

edit in interface EditableAlignment

Throws:

ChangeVetoException

shiftAtAlignmentLoc

public void shiftAtAlignmentLoc(Object label,
                                Location loc,
                                int offset)
                         throws ChangeVetoException,
                                IllegalAlignmentEditException,
                                IndexOutOfBoundsException

loc in this case is the Alignment Location

Specified by:

shiftAtAlignmentLoc in interface EditableAlignment

Throws:

ChangeVetoException

IllegalAlignmentEditException

IndexOutOfBoundsException

shiftAtSequenceLoc

public void shiftAtSequenceLoc(Object label,
                               Location loc,
                               int offset)
                        throws ChangeVetoException,
                               IllegalAlignmentEditException,
                               IndexOutOfBoundsException

loc in this case is the SymbolList Location

Specified by:

shiftAtSequenceLoc in interface EditableAlignment

Throws:

ChangeVetoException

IllegalAlignmentEditException

IndexOutOfBoundsException

removeGaps

public void removeGaps(GappedSymbolList seq,
                       int start,
                       int length)

because there is a bug in GappedSymbolList

allGaps

protected boolean allGaps(SymbolList seq,
                          int start,
                          int end)

make sure that all Symbols in this range are gaps

resetRange

protected void resetRange()
                   throws ChangeVetoException

check that begining is at 1 otherwise shift everything over

Throws:

ChangeVetoException

shiftAll

protected void shiftAll(int offset)
                 throws ChangeVetoException

Throws:

ChangeVetoException

shift

protected void shift(Object label,
                     int offset)
              throws ChangeVetoException

moves the whole sequence

Throws:

ChangeVetoException

greater

protected int greater(int x,
                      int y)

lesser

protected int lesser(int x,
                     int y)

getAE

protected AlignmentElement getAE(Object label)
                          throws NoSuchElementException

Throws:

NoSuchElementException

posInSeq

protected int posInSeq(Object label,
                       int column)
                throws NoSuchElementException,
                       IndexOutOfBoundsException

get the position in the sequence corresponding to the postion within the alignment

Throws:

NoSuchElementException

IndexOutOfBoundsException

locInSeq

protected Location locInSeq(Object label,
                            Location viewLoc)
                     throws NoSuchElementException,
                            IndexOutOfBoundsException

Throws:

NoSuchElementException

IndexOutOfBoundsException